Archive for Angus Thies

So just like that were at the end of it all (well almost). This week was a complete blur of data reconfiguration, R script, poster formatting, and presentation rehearsal. This was actually the very first scientific poster I ever had to make and present so the week was a bit stressful haha. I was really happy with the result however; I think it was a success! Getting to hear about everyone’s research in detail was also a really interesting experience. It’s hard not to get caught up in only your own research this summer so it was incredibly refreshing to see everyone else’s results.

In the celebratory spirit, we all went over to the Great Albacore Tune BBQ Challenge by the NOAA docks today. For just $12 each we got to try bottomless albacore recipes including pulled tuna, tuna gazpacho, and tuna teriyaki with pineapple. Best money I’ve spent in a very long time; absolutely delicious! As I’m writing this blog a thought occurred to me: is albacore tuna sustainably harvested in the North Pacific? To try and relieve the guilt I suddenly felt about having a belly full of delicious fish I turned to one of my favorite websites: seafoodwatch.org. Seafood Watch is a program run by the Monterey Bay Aquarium. In the site’s own words: “Our recommendations help you choose seafood that’s fished or farmed in ways that have less impact on the environment.” It allows visitors to the site to lookup seafood items (e.g. albacore tuna) based on where you bought it (e.g. North Pacific, domestic) and the site gives the source a rating based on sustainability. In the North Pacific luckily, Albacore tuna populations are being sustainably fished. Phew. Besides just making us feel guilty about our food choices, the website also provides ‘good alternatives’ to users. For example, my favorite seafood is scallops. When I search for this item I got three results, two east coast sources and one from Alaska. Those from the east coast are marked as ‘good alternatives’ but the most sustainable option is to but those from Alaska which was dubbed the ‘best choice.’ If you haven’t ever been to seafoodwatch.org I highly recommend you take a peak next time you’re setting a menu!

Happy Sunday folks! Let’s start with some of the nitty-gritty science stuff. This Friday I completed my last fieldwork in Yaquina Bay. Amy and I took a trip upriver to three eelgrass beds where we collected water, sediment, and eelgrass samples for processing. For the first time this summer the processing went completely smoothly! Nothing got mixed-up and the new lab layout gave us tons of space (we totally reorganized this week in anticipation of a visit from an EPA bigwig). It appears that, based on our preliminary data, eelgrass is a massive reservoir of Enterococci (a fecal indicator bacteria). What’s more, the majority of this bacteria is loosely-attached to the plant via biofilms and could be easily resuspended by wave action or storm energy. This finding could have big implications on future work as storm-based water sampling could be providing skewed levels of indicator bacteria due to resuspension. This would falsely indicate levels of fecal matter in the bay. I know you’re all hooked but you’ll have to wait until my poster is complete to learn the whole story (I can’t go spoil the results for you).

Speaking of posters and presentations, there’s only 5 days until the final symposium! How’d that happen?!? This coming week is going to involve a LOT of figure-making and R script…I know, sounds like a party, right? I am actually excited to see if there are any interesting findings however! We shall see.

On a very non-Sea Grant note I want to take a second to talk about an issue that I feel doesn’t get addressed enough in our fast-paced culture: mental health. It’s not a very popular topic and it’s slightly taboo in our culture to discuss mental health; maybe it’s because we associate the term with ‘crazy’ or ‘illness.’ Regardless, it’s a topic that we should all stop and think about every so often. I think it’s especially relevant for those of us thinking about graduate school to take time and evaluate how we make our choices and if they are good for us. I don’t just mean good for us professionally but also mentally and personally. I know that I’ve felt immense pressure to go to grad school ASAP and get my degree ASPA and get a post-doc ASAP and get a job ASAP and produce research ASAP…it’s exhausting just to think about it all. The truth is that this thought process doesn’t leave much room for our own personal growth or happiness. I would argue that making choices for mental health reasons should be just as important as, if not more so, than academic reasons. Being happy isn’t a luxury that’s earned with success; it’s a right that we all should take the time to exercise in our lives no matter what are professional goals are. Invest in friendships. Forge healthy relationships. Bottom line: take care of yourself first.

So my mentor, Amy, has been gone since July 21st at a conference in Michigan and left me with a to-do list for my time alone. Although I was secretly terrified at the prospect (I’m an intern all alone in the wilderness) this week was incredibly fulfilling. Not only did I not screw anything up (fingers crossed) but I was able to get through all the tasks and start playing with the data we’ve collected so far this summer. Stay tuned for all the earth-shattering announcements to be made at the final symposium. I also learned how to use an oven-furnace this week; Katie, an EPA GRO intern, was kind enough to teach me and showed me how not to burn down the building. I also started teaching myself the stats program R using an online tool called Swirl. Super fun stuff. My week rounded out with a quick trip back to Boston for a funeral in western MA. Despite the circumstances it was great to see my parents and brother again (I haven’t been home since December so this was long overdue). The plane rides also gave me plenty of time to perfect my mad-coding skills in R. I’m not entirely sure what this week has in store for me but I’m looking forward to playing with some more data and getting my poster ready!

Nothing huge to report this week! Monday and Tuesday were dedicated to getting the lab prepped for a field sampling trip to Tillamook Bay on Wednesday. That mostly involved labeling lots of sample bags/bottles and filling a plethora of tubes with 0.3g of glass beads to be used in DNA extractions next week. Although the work is fairly tedious it does payoff to get to spend a whole morning out on the water! The sampling actually went well this time and the hovercraft didn’t have any terminal malfunctions until the very last sample site. We were able to collect water, nutrient, sediment, and eelgrass samples from 7 sites in all. The down side of getting that many sites is that it takes an obscene amount of time to process the samples when we get back to the lab that afternoon. Overall, it was a 14hr day once we got the water filtered and the sediment and eelgrass rinsed. On the bright side I only had half days on Thursday and Friday so there was some time to catch up on sleep and go for a run! I spent those days scraping epiphytes off of eelgrass leaves and preparing samples for moisture content analysis. All things considered it was a good week in the office!

The big event this week that has been on my mind is that I’ve decided, with the support of my school mentor and Amy, to rework a research paper I authored last fall into a publishable manuscript. On my semester abroad with the School for Field Studies in the Turks and Caicos, BWI I spent a month doing my own research on the interactions of two groups of indicator species (2 Acroporid corals, A. palmata and A. cervicornis, and the long-spined sea urchin, Diadema antillarum). I ended up finding some interesting relationships between these three species and I would love to have this work published in Marine Ecology Progress Series. I know this is going to be a long road but I’m not too stressed (which is VERY unusual for me haha). I’ve already done all the heavy lifting so I just need to rerun some statistics, generate better figures, do general editing, and reformat the manuscript. My current plan is to ask a professor at UCSD to co-author with me and have them help me with the process. Who knows, it might just work out!

Another week another adventure out here in Oregon! So not only did we have our mid-summer check in this Friday but we also had the chance to go camping in Willamette National Forest this weekend. It felt amazing to be back out in the woods just hiking around again. The last time I was able to go camping was in Laguna National Forest outside of San Diego; needless to say there was a tad more desert involved. To say the least, it’s the polar opposite of San Diego, or the rest of the Oregon coast for that matter. Old growth forest clings to the rolling hills as far as the eye can see and the far-off peaks of the Three Sisters and Mt. Washington were visible from the trails. It even reached the high 70s (gasp) and felt like real summer for a few days. It was simply spectacular and I would have been happy to skip work this entire week to stay and hike around some more. I’m sure the rest of this week’s blog posts will revolve around the weekend’s hikes so I’ll let them fill in the rest of the details about the natural side of things.

The pics are of Tamolich Pool, some streams below Klamath Falls, and all of us idiots posing in front of South Sister on our hike to Moraine Lake.

On a more ‘sciencey’ note Amy, TChris, and I went water sampling this week. We drove up to the Tillamook watershed and sampled the five main tributary rivers that drain into the bay. Although we were only taking nutrient, microbial, and parameter samples it was a solid 13hr day. Couldn’t have asked for better weather though and the day did of course involve a trip to the Tillamook Creamery so overall it was a great day!

The pics are of our very full car out on the field sampling trip and of an IDEXX tray that has been incubated to test for the presence of Enterococcus spp.

So why is the 4th of July, 1776 so famous? The obvious answer is that it’s the day that the U.S. Continental Congress declared independence from Great Britain. Wait, nope, that happened on july 2nd. Oh wait duh, it must have been the day that we started the revolutionary war. Nope, you’re wrong again. That happened a year earlier in 1775. OK so was it when a draft of the constitution was written or when it was signed?? Wrong and wrong-er. That was June and August of 1776. Ok so what the heck really happened on July 4th, 1776? Congress did something they haven’t done since the 1960s: they agreed on something. To be specific, they agreed on the final draft of the document. Super exciting. So why do we celebrate the 4th? Following the war of 1812 (yes there was a war in 1812, bet you all didn’t remember that from middle school history) there was great ideological division in the United States. Copies of the declaration were circulated around the nation with the date July 4th at the top. This inspirited national unity around the date (incidentally Thomas Jefferson and John Adams also died on July 4th, 1826 so that may have helped).

A lot has happened since then though. The liberty bell cracked beyond repair while ringing to celebrate Washington’s birthday in 1846, the Civil War divides the nation in 1861, the statue of liberty is gifted to the U.S. by France and erected in 1886, the U.S. and Spain go to war briefly (you probably also forgot about that), the Panama Canal is established in 1903, World Wars I and II erupt in 1914 and 1939, man walks on the moon in 1969, and finally and most importantly, the US EPA is founded by Richard Nixon on December 2, 1970.

The 4th of July these days is still a cause for celebration. Festivities usually involve buying cheap meats and American flag apparel from Walmart, public intoxication on beaches and pontoon boats, BBQs, cheap beer, and of course fireworks. Mostly though it’s a holiday for spending time with friends and family. My family’s usual tradition is to go up to Old Orchard Beach, ME with a bunch of family friends. This is the first year I couldn’t make it but those of us at Hatfield, including Collin who drove up here for a night, have been having a blast. We went out to the Sandbar on Friday, drove down to Otter Point yesterday, and had a huge communal BBQ courtesy of Walmart (pics included below). Needless to say I’m excited to see what the actual 4th brings.

Since I do feel somewhat obligated to talk shop on my Sea Grant blog post here we go: this week at the office was pretty sweet for three reasons. First, not only did I learn how to extract DNA for qPCR but I didn’t even screw it up (I don’t think…I’ll get back to you on that one)! Second, Amy has also been helping me to put together my own project I can work on during the down time in our sampling. Since I’m definitely more interested in biology than general water quality, my project is investigating on the role of Eelgrass (Zostera marina) in promoting the growth of Enterococci ssp. (a fecal indicator bacteria). Almost all surfaces in the natural world have biofilms on them as a result of bacterial growth. Eelgrass is no exception and the aquatic habitat it lives in serves to expedite the growth of this film. Suspended bacteria can adhere to the plant’s leaves and reproduce rapidly. I want to know if these indicator bacteria can become suspended due to leaf decay, storm events, or tidal flow. If so, this resuspension could be contributing to the exceedance of regulatory limits for indicator bacteria thereby yielding a false positive. Third, I got to go on some unplanned fieldwork this Friday in Tillamook with Jess and one of her mentors, Jody. Although I couldn’t reach the site I needed to due to a higher than usual low tide, it was a gorgeous day and I was able to collect some samples for my own project. Jody did make us go get ice cream and lunch at the Blue Heron though…that was pretty rough.

All things considered it’s been a pretty great week in Oregon but how time flies…

Here are the pics from fieldwork, Devil’s Well, the Otter drive, and our glorious BBQ:

So week two is already done…hard to believe; this summer is flying by. A lot has happened though since my last post! First, I got stuck in the mud haha. I guess it was bound to happen at some point. We went out on Tuesday for our first field sampling trip to Tillamook Bay (2 hrs north of Newport). Since we needed to cross both water and mud flats during our sampling, we elected to use one of the EPA’s hovercrafts. Yes, it was as awesome as it sounds. Everything was going great for the first hour or so! We got to 3 sites and collected water, nutrient, sediment, and eelgrass samples at each. Then we hit our first speed bump. The pillow-block (the part of the engine that holds the driveshaft of the propeller in place) failed in spectacular fashion due to old age. As a result, the belt connecting the driveshaft to the engine lost tension and we were left dead in the bay. Thankfully we were fairly close to shore and the tide was coming in so we started paddling towards shore. With some luck we made it to shallow water that was near our 4th sampling site so, like any good scientists, we stopped and took some more samples. We resumed pushing the hovercraft when we had finished. As it turned out, we had broken down very close to the Pacific Oyster factory and there was a makeshift boat-ramp by their jetty. That was when our luck ran out: to get to the ramp we would need to pull the hovercraft across 300ft of mudflat. After 10 minutes of yanking and tugging on the hovercraft’s bowline I found my right leg buried in mud up to the knee and solidly stuck. Once I had been dug out we resumed our struggle but my boss took my place being stuck. After an hour of this repeated pulling, getting stuck, and digging each other free we had only moved 50ft. To make a very long story short it took us 3 hours to get to the boat-ramp and it was only with the help of the tide and some very nice folks from the Oregon Department of Fish and Wildlife’s Tillamook Office did we get that head of metal back on its trailer and back to Newport. On the bright side I did get some pretty stellar ice cream at Tillamook Creamery.

Second, I processed a LOT of samples from our field collections. Every water and eelgrass sample gets filtered for DNA for qPCR (quantitative polymerase chain reaction) so we can start to identify whose fecal bacteria have made it into the bay (human, cow, chicken, or otherwise). Sediment, water, and eelgrass samples also need to be diluted down for IDEXX testing; this detects the presence of certain indicator bacteria such as Enterococci ssp. and fecal coliform and generates the most probable number of bacteria per 100ml of sample. We also enrich many of the samples with growth media to try and grow Salmonella, E. coli, etc. to see if they are present in the samples.

Third and finally, I started doing some research for my own side project that will feed into my work at the EPA: how eelgrass biology could play a role in enabling the retention of indicator bacteria in the Bay. I’m mostly reading papers right now but I’m going to start work on a lit review next week. Hopefully it works out and I can use it as part of my poster!

That’s all for this week! I’ve put a link to some of the fieldwork pictures below, sadly nobody thought to take a picture while we were struggling in the mud haha.

So I’ve read a lot about different kinds of poop these past few days…cow, bird, elk, and human to be specific (yes, there is a difference). Why? Because my mentor (Amy) is focusing on determining the sources of feces that contribute to the microbial load in Tillamook Bay. Although the details are still in flux, the current plan for the summer is to take water and sediment samples from various estuaries that empty into the bay and gather nutrient, chlorophyll, and microbial data. The microbial data Amy is looking to collect is specifically regarding fecal indicator bacteria (FIB), microbes that are found in feces that can signal the potential presence of other harmful pathogens in the water. We will also be using qPCR to determine the abundance of specific genetic markers from certain microbes in order to do microbial source tracking (MST). MST allows us to determine whose poop is where and how much of it there is. I’m sure that I’ll learn more as the next week unfolds and we do some field work for the first time. If time permits I’m also going to be able to work on my own side-project related to microbes in the Tillamook Bay; I’m thinking of looking at the concentrations of microbes in oyster gut tissues or on the biofilm produced by eelgrass, Zostrea marina. I’m getting really excited for all the data to start coming it, it’s going to be a cool time at the EPA!

On a non-science related note Newport is pretty sweet! It feels a lot like Boston (my hometown) and Maine; it’s great to be around actual trees instead of being in the SoCal desert. Newport itself is a quaint little town that really only exists on one main street by the bay; it’s a nice small-town feel.

Today we kicked off our 2016 Summer Scholars season with an orientation for the 10 undergraduates who will be spending their summer working on research and public engagement projects with natural resource agencies on the Oregon coast: Angus Thies, Lexi Brewer, Skyler Elmstrom, Claire Mullaney, Erin Horkin, Stephanie Ng, Collin Williams, Edward Kim, Justin Dalaha and Jessica Vaccare.

This is the largest class of Summer Scholars we’ve hosted to date, and we look forward to reading their posts about their experiences in our Sea Grant Scholars blog.